Author ORCID Identifier

https://orcid.org/0000-0002-2956-9781 : James W. Gauld

Document Type

Article

Publication Date

2018

Publication Title

The Journal of Physical Chemistry

Volume

122

Issue

3

First Page

1092

Last Page

1101

DOI

10.1021/acs.jpcb.7b10254

Abstract

Archaeal threonyl-tRNA synthetase (ThrRS) possesses an editing active site wherein tRNAThr that has been misaminoacylated with serine (i.e., Ser-tRNAThr) is hydrolytically cleaved to serine and tRNAThr. It has been suggested that the free ribose sugar hydroxyl of Ado76 of the tRNAThr(Ado762′OH) is the mechanistic base, promoting hydrolysis by orienting a nucleophilic water near the scissile Ser-tRNAThr ester bond. We have performed a computational study, involving molecular dynamics (MD) and hybrid ONIOM quantum mechanics/molecular mechanics (QM/MM) methods, considering all possible editing mechanisms to gain an understanding of the role played by Ado762′OH group. More specifically, a range of concerted or stepwise mechanisms involving four-, six-, or eight-membered transition structures (total of seven mechanisms) were considered. In addition, these seven mechanisms were fully optimized using three different DFT functionals, namely, B3LYP, M06-2X, and M06-HF. The M06-HF functional gave the most feasible energy barriers followed by the M06-2X functional. The most favorable mechanism proceeds stepwise through two six-membered ring transition states in which the Ado762′OH group participates, overall, as a shuttle for the proton transfer from the nucleophilic H2O to the bridging oxygen (Ado763′O) of the substrate. More specifically, in the first step, which has a barrier of 25.9 kcal/mol, the Ado762′-OH group accepts a proton from the attacking nucleophilic water while concomitantly transferring its proton onto the substrates C–Ocarb center. Then, in the second step, which also proceeds with a barrier of 25.9 kcal/mol, the Ado762′-OH group transfers its proton on the adjacent Ado763′-oxygen, cleaving the scissile Ccarb–O3′Ado76 bond, while concomitantly accepting a proton from the previously formed C–OcarbH group.

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